Thanks David. (Now I see further back in the thread where the file in question was posted in google drive!)
On Tue, Apr 15, 2014 at 3:14 PM, David Shteynberg < [email protected]> wrote: > Hey Jimmy, > > I checked in a fix today. > > Cheers, > -David > > > On Tue, Apr 15, 2014 at 3:05 PM, Jimmy Eng <[email protected]> wrote: > >> Will, >> >> Can you send me a copy of your cidtest.sqt file and I'll look into it >> when I get a chance? Compress/zip the 11Mb file and either email it to me >> or make it available as a download link. Thanks. >> >> - Jimmy >> >> >> >> On Tue, Apr 15, 2014 at 11:30 AM, Will Fondrie <[email protected]>wrote: >> >>> >>> I've been playing around with the -r flag but I don't think its >>> converting the entire file. It is possible that I just have a >>> misunderstanding of what the -r flag is doing and what the results should >>> be. >>> >>> When I use: >>> Sqt2XML -r 10 cidtest.sqt >>> >>> The output is a pep.xml file that is only 24 Kb in size. >>> >>> Then, when I use: >>> Sqt2XML -r 1 cidtest.sqt >>> >>> The output is a pep.xml file that is 1.9 Mb. >>> >>> However both of these seem to small to contain the information of my 11 >>> Mb cidtest.sqt file. Also, I would have thought that the -r 10 command >>> should result in a larger file than the -r 1 command. >>> >>> Thank you, >>> Will >>> >>> On Monday, April 14, 2014 4:44:48 PM UTC-4, David Shteynberg wrote: >>> >>>> The problem is a small bug in this tool that requires you to set the -r >>>> flag . -r sets the max rank of reported peptides: >>>> >>>> Try: >>>> >>>> Sqt2XML -r 10 cidtest.sqt >>>> >>>> >>>> Thanks! >>>> >>>> -David >>>> >>>> >>>> On Mon, Apr 14, 2014 at 11:50 AM, Will Fondrie <[email protected]>wrote: >>>> >>>>> Here's a Google Drive link to the cidtest.sqt file that I'm working >>>>> with. >>>>> >>>>> https://drive.google.com/file/d/0B0ATSXjfowrdV2ZDQXlTbEMwdVU/ >>>>> edit?usp=sharing >>>>> >>>>> The file was too big to attach to this message. It was generated as >>>>> the output from a ProLuCID search using a *.ms2 file. This was my first >>>>> time trying to convert the *.sqt files from this tool (and in general). >>>>> >>>>> Thanks for the help and the quick reply! >>>>> >>>>> -Will >>>>> >>>>> >>>>> On Monday, April 14, 2014 2:34:38 PM UTC-4, David Shteynberg wrote: >>>>> >>>>>> I can't tell without looking at the file but my best guess is one of >>>>>> the following: >>>>>> >>>>>> A. The sqt could be malformed or corrupted, has this tool generated >>>>>> sqt that you could convert before or was this your first try? >>>>>> >>>>>> B. It cannot find the data file mzML or mzXML per the message >>>>>> >>>>>> If you share the file I could potentially identify the issue. >>>>>> >>>>>> -David >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Mon, Apr 14, 2014 at 11:18 AM, Will Fondrie <[email protected]>wrote: >>>>>> >>>>>>> Hi everyone, >>>>>>> >>>>>>> I am trying to convert *.sqt files from my ProLuCID searches into >>>>>>> *.pep.XML using the Sqt2XML tool. >>>>>>> The command I am running is: >>>>>>> >>>>>>> > Sqt2XML cidtest.sqt >>>>>>> >>>>>>> Where "cidtest.sqt" is my example search result, and my >>>>>>> sequest.params file is in the same directory. However, I get the >>>>>>> following >>>>>>> output: >>>>>>> >>>>>>> params file here: sequest.params >>>>>>> attempting to read mzXML/mzML: Unknown file type. No file loaded. >>>>>>> Done. File created: cidtest.pep.xml >>>>>>> >>>>>>> When I check the *.pep.xml file that was created, it is not nearly >>>>>>> as large as it should be. Any idea's on what I'm doing wrong? >>>>>>> >>>>>>> Thank you, >>>>>>> Will >>>>>>> >>>>>>> -- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "spctools-discuss" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to [email protected]. >>>>>>> To post to this group, send email to [email protected]. >>>>>>> >>>>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>> >>>>>> >>>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
